The goal of this proposed ORINCON research is the development of new tools and techniques for biological sequence analysis based on the application of several promising new signal processing technologies. In particular we hope to develop faster, more accurate, and more robust methods for biological sequence comparison, more compact representation and storage techniques for derived nucleotide or amino acid sequences, and more reliable procedures for the automatic identification of specific functional regions of the genome, such as promoter sites, intron regions, or exon regions. In Phase I of this effort, we will restrict our attention to the study of wavelet transform techniques for sequence comparison, sequence representation, and site recognition. Wavelet transforms have received a great deal of attention recently and have been shown to be superior to traditional Fourier-based analysis techniques in many respects. Of particular interest for sequence analysis applications are finite-field wavelet transforms, which are ideally suited for the analysis of signals (or sequences) that take values in a finite field rather than the fields of real or complex numbers. Since any encoding of a nucleotide or amino acid sequence can be represented quite naturally in a finite field, this technique is very appealing.